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C
CABAminoAcidGenerator
- Class in
ProGAL.proteins.structure.generators
CABAminoAcidGenerator()
- Constructor for class ProGAL.proteins.structure.generators.
CABAminoAcidGenerator
calcRoots()
- Method in class ProGAL.math.
Polynomial
Find the roots of the polynomial.
calcRoots(double[])
- Static method in class ProGAL.math.
Polynomial
Find the roots of the polynomial specified by the parameters.
calcRoots(double, double, double)
- Static method in class ProGAL.math.
Polynomial
Find the roots of a second degree polynomial.
calcRoots(double, double, double, double)
- Static method in class ProGAL.math.
Polynomial
Find the roots of a third degree polynomial.
CALoopStructure
- Class in
ProGAL.proteins.beltaStructure.loop
CALoopStructure(SecondaryStructure, int, int)
- Constructor for class ProGAL.proteins.beltaStructure.loop.
CALoopStructure
CALoopStructure.SegmentStructure
- Class in
ProGAL.proteins.beltaStructure.loop
Camera
- Class in
ProGAL.geom3d.viewer
Represents a camera located somewhere in the scene.
CanonicalSheet
- Class in
ProGAL.proteins.beltaStructure
CanonicalSheet(SheetTopology)
- Constructor for class ProGAL.proteins.beltaStructure.
CanonicalSheet
capWithDiscs(PointList)
- Method in class ProGAL.geom3d.volumes.
InfCylinder
capWithHalfSpheres(PointList)
- Method in class ProGAL.geom3d.volumes.
InfCylinder
capWithHalfSpheres(LSS, LSS)
- Method in class ProGAL.geom3d.volumes.
InfCylinder
CARTOON
- Static variable in class ProGAL.proteins.viewer.
PDBFileViewer
CBond
- Class in
ProGAL.proteins.structure
CBond(Atom, Atom)
- Constructor for class ProGAL.proteins.structure.
CBond
CEdge
- Class in
ProGAL.geom3d.complex
CEdge(CVertex, CVertex)
- Constructor for class ProGAL.geom3d.complex.
CEdge
cellFromPoint(Point)
- Method in class ProGAL.dataStructures.rangeSearching.
GridMap
center()
- Method in class ProGAL.geom2d.
Circle
center
- Variable in class ProGAL.geom3d.
Rectangle
centerCamera()
- Method in class ProGAL.geom2d.viewer.
J2DScene
Center the view on the objects in the scene
centerCamera()
- Method in class ProGAL.geom3d.viewer.
J3DScene
Sets the location that the camera looks at to the center of all the shapes added to the scene.
centerCamera(Point)
- Method in class ProGAL.geom3d.viewer.
J3DScene
chain
- Variable in class ProGAL.proteins.
PDBFile.AtomRecord
A character identifying the chain
chain
- Variable in class ProGAL.proteins.
PDBFile.TerRecord
ChainTree
- Class in
ProGAL.proteins.chainTree
A chain tree representation of the structure of a protein sub-chain.
ChainTree(PrimaryStructure)
- Constructor for class ProGAL.proteins.chainTree.
ChainTree
Construct a chain tree representing the structure of the specified sequence.
ChainTree(PrimaryStructure, int, int)
- Constructor for class ProGAL.proteins.chainTree.
ChainTree
Construct a chain tree representing the structure of the residues in the specified interval.
ChainTreeLoop
- Class in
ProGAL.proteins.beltaStructure
ChainTreeLoop(SecondaryStructure, int, int)
- Constructor for class ProGAL.proteins.beltaStructure.
ChainTreeLoop
changeAlpha(double)
- Method in class ProGAL.geom3d.complex.alphaComplex.
Node
changeDeath(double)
- Method in class ProGAL.geom3d.complex.alphaComplex.
Node
checkTessels()
- Method in class ProGAL.geomNd.complex.delaunayComplex.
BowyerWatson
Checks that all tetrahedra comply with the Delaunay-criteria.
checkTetrahedra()
- Method in class ProGAL.geom3d.complex.delaunayComplex.
DelaunayComplex
Checks that all tetrahedra comply with the Delaunay-criteria.
checkTetrahedra()
- Method in class ProGAL.geom3d.complex.tessellation.
DelaunayTessellation
Checks that all tetrahedra comply with the Delaunay-criteria.
Circle
- Class in
ProGAL.geom2d
Circle(Point, double)
- Constructor for class ProGAL.geom2d.
Circle
Construct a circle with the given center and radius.
Circle(Circle)
- Constructor for class ProGAL.geom2d.
Circle
Constructs a circle that is a copy of a given circle
Circle(Point, Point)
- Constructor for class ProGAL.geom2d.
Circle
Circle(Point, Point, Point)
- Constructor for class ProGAL.geom2d.
Circle
Creates circle through 3 given points.
Circle(Circle, Circle)
- Constructor for class ProGAL.geom2d.
Circle
Circle(Circle, Circle, Circle)
- Constructor for class ProGAL.geom2d.
Circle
Circle(Triangle)
- Constructor for class ProGAL.geom2d.
Circle
Circle
- Class in
ProGAL.geom3d
A circle in (x,y,z)-space represented by a center-point, a radius and a normal-vector.
Circle(Point, double, Vector)
- Constructor for class ProGAL.geom3d.
Circle
Circle(Point, Point, Vector)
- Constructor for class ProGAL.geom3d.
Circle
A circle with given center through a given point and with specified normal vector
Circle(Point, Point, Point)
- Constructor for class ProGAL.geom3d.
Circle
Circle in the plane through p0, p1, p2
circumcenter()
- Method in class ProGAL.geom3d.
Triangle
Return the circumcenter of the triangle.
circumCenter()
- Method in class ProGAL.geom3d.volumes.
Tetrahedron
Find the center of the circumscribing sphere.
circumradius(Point, Point, Point, Point)
- Method in class ProGAL.geom3d.predicates.
ExactJavaPredicates
circumradius(Tetrahedron)
- Method in class ProGAL.geom3d.predicates.
ExactJavaPredicates
circumradius(Point, Point, Point)
- Method in class ProGAL.geom3d.predicates.
ExactJavaPredicates
circumradius(Triangle)
- Method in class ProGAL.geom3d.predicates.
ExactJavaPredicates
circumradius(Point, Point, Point, Point)
- Method in class ProGAL.geom3d.predicates.
ExactNativePredicates
circumradius(Tetrahedron)
- Method in class ProGAL.geom3d.predicates.
ExactNativePredicates
circumradius(Point, Point, Point)
- Method in class ProGAL.geom3d.predicates.
ExactNativePredicates
circumradius(Triangle)
- Method in class ProGAL.geom3d.predicates.
ExactNativePredicates
circumradius(Point, Point, Point, Point)
- Method in class ProGAL.geom3d.predicates.
InexactJavaPredicates
circumradius(Tetrahedron)
- Method in class ProGAL.geom3d.predicates.
InexactJavaPredicates
circumradius(Point, Point, Point)
- Method in class ProGAL.geom3d.predicates.
InexactJavaPredicates
circumradius(Triangle)
- Method in class ProGAL.geom3d.predicates.
InexactJavaPredicates
circumradius(Point, Point, Point, Point)
- Method in class ProGAL.geom3d.predicates.
InexactRegularJavaPredicates
circumradius(Tetrahedron)
- Method in class ProGAL.geom3d.predicates.
InexactRegularJavaPredicates
circumradius(Point, Point, Point)
- Method in class ProGAL.geom3d.predicates.
InexactRegularJavaPredicates
circumradius(Triangle)
- Method in class ProGAL.geom3d.predicates.
InexactRegularJavaPredicates
circumradius(Point, Point, Point, Point)
- Method in class ProGAL.geom3d.predicates.
Predicates
circumradius(Tetrahedron)
- Method in class ProGAL.geom3d.predicates.
Predicates
circumradius(Point, Point, Point)
- Method in class ProGAL.geom3d.predicates.
Predicates
circumradius(Triangle)
- Method in class ProGAL.geom3d.predicates.
Predicates
circumradius()
- Method in class ProGAL.geom3d.
Triangle
Return the circumradius of the triangle.
circumRadius()
- Method in class ProGAL.geom3d.volumes.
Tetrahedron
Calculate the radius of the circumsphere.
circumSphere
- Variable in class ProGAL.geom3d.tessellation.BowyerWatson.
Tet
circumSphere()
- Method in class ProGAL.geom3d.volumes.
Tetrahedron
Find the circumscribing sphere
clear()
- Method in class ProGAL.dataStructures.
DLCyclicList.DLNode
Clears the node and returns its object
clear()
- Method in class ProGAL.dataStructures.
Heap
remove all elements
clear()
- Method in class ProGAL.dataStructures.
Set
click()
- Method in interface ProGAL.dataStructures.viewer.
InteractiveBinaryTree
click()
- Method in class ProGAL.geom3d.complex.alphaComplex.
Node
ClickListener
- Interface in
ProGAL.geom3d.viewer
clone()
- Method in class ProGAL.geom2d.
LineSegment
clone()
- Method in class ProGAL.geom2d.
LSC
clone()
- Method in class ProGAL.geom2d.
Point
clone()
- Method in class ProGAL.geom2d.
Vector
clone()
- Method in class ProGAL.geom3d.
LineSegment
Returns a deep clone of this line segment.
clone()
- Method in class ProGAL.geom3d.
Point
Return a new object that equals this object.
clone()
- Method in class ProGAL.geom3d.
PointList
Get a shallow copy of this list.
clone()
- Method in class ProGAL.geom3d.surface.
ParametricParaboloid
clone()
- Method in class ProGAL.geom3d.surface.
ParametricPlane
clone()
- Method in class ProGAL.geom3d.surface.
ParametricSurface
clone()
- Method in class ProGAL.geom3d.
Triangle
clone()
- Method in class ProGAL.geom3d.
Vector
Create a clone of this vector.
clone()
- Method in class ProGAL.geom3d.volumes.
Cone
clone()
- Method in class ProGAL.geom3d.volumes.
Cylinder
clone()
- Method in class ProGAL.geom3d.volumes.
Lens
clone()
- Method in class ProGAL.geom3d.volumes.
LSS
clone()
- Method in class ProGAL.geom3d.volumes.
OBB
clone()
- Method in class ProGAL.geom3d.volumes.
RSS
clone()
- Method in class ProGAL.geom3d.volumes.
Sphere
Returns a deep clone of this sphere.
clone()
- Method in class ProGAL.geom3d.volumes.
Tetrahedron
clone()
- Method in interface ProGAL.geom3d.volumes.
Volume
Make a deep clone this volume.
clone()
- Method in class ProGAL.geomNd.
Point
clone()
- Method in class ProGAL.geomNd.
PointList
Get a shallow copy of this list.
clone()
- Method in class ProGAL.geomNd.
Vector
Create a clone of this vector.
clone()
- Method in class ProGAL.math.
Matrix
Returns a clone of this matrix.
clone()
- Method in class ProGAL.math.
Matrix3x3
clone()
- Method in class ProGAL.proteins.beltaStructure.sheet.
ParametricSurface
clone()
- Method in class ProGAL.proteins.structure.
AminoAcid
clone()
- Method in class ProGAL.proteins.structure.
Atom
clone()
- Method in class ProGAL.proteins.viewer.
CoilSurface
clone()
- Method in class ProGAL.proteins.viewer.
HelixSurface
clone()
- Method in class ProGAL.proteins.viewer.
StrandSurface
closeCCD(Point[], int)
- Method in class ProGAL.proteins.chainTree.
ChainTree
Perform cyclic coordinate descent on this chain so the positions of the end-atoms overlap with those specified in the
target
-array.
closestSegmentPoint(Point, Point, Point, Point)
- Static method in class ProGAL.geom3d.
Rectangle
28HOps at most.
closestSegmentPoint(Point, Point, Point)
- Static method in class ProGAL.geom3d.
Rectangle
closestSegmentPoint(LSS)
- Method in class ProGAL.geom3d.volumes.
LSS
CN_ClashLowerBound
- Class in
ProGAL.proteins.beltaStructure.bnb.lowerBounds
CN_ClashLowerBound(double[])
- Constructor for class ProGAL.proteins.beltaStructure.bnb.lowerBounds.
CN_ClashLowerBound
CoilDatabase
- Class in
ProGAL.proteins.beltaStructure.loop
CoilDatabase()
- Constructor for class ProGAL.proteins.beltaStructure.loop.
CoilDatabase
CoilSurface
- Class in
ProGAL.proteins.viewer
collinear(Point, Point, Point)
- Static method in class ProGAL.geom2d.
Point
collinear(Point, Point, Point)
- Static method in class ProGAL.geom3d.
Point
Returns true if three points are on the same line.
collinear(Point, Point, Point)
- Static method in class ProGAL.geomNd.
Point
Combinatorics
- Class in
ProGAL.math
A wrapper for static combinatorial helper functions.
Combinatorics()
- Constructor for class ProGAL.math.
Combinatorics
CombinatoricsTest
- Class in
ProGAL.math.test
CombinatoricsTest()
- Constructor for class ProGAL.math.test.
CombinatoricsTest
COMP_EQUAL
- Static variable in interface ProGAL.dataStructures.
SortTool
COMP_GRTR
- Static variable in interface ProGAL.dataStructures.
SortTool
COMP_LESS
- Static variable in interface ProGAL.dataStructures.
SortTool
compare(Point, Point)
- Method in class ProGAL.dataStructures.rangeSearching.rangeTree.
PointDimensionComparator
compare(Object, Object)
- Method in interface ProGAL.dataStructures.
SortTool
compare(Object, Object)
- Method in class ProGAL.dataStructures.
SortToolDouble
compare(Object, Object)
- Method in class ProGAL.dataStructures.
SortToolInteger
compare(Object, Object)
- Method in class ProGAL.dataStructures.
SortToolLineSegment2dAroundCommonPoint
compare(Object, Object)
- Method in class ProGAL.dataStructures.
SortToolLineSegment2dByLength
compare(Object, Object)
- Method in class ProGAL.dataStructures.
SortToolPoint2dAroundOrigo
compare(Object, Object)
- Method in class ProGAL.dataStructures.
SortToolPoint2dAroundPoint
compare(Object, Object)
- Method in class ProGAL.dataStructures.
SortToolPoint2dDistance
compare(Object, Object)
- Method in class ProGAL.dataStructures.
SortToolPoint2dXY
compare(Object, Object)
- Method in class ProGAL.dataStructures.
SortToolString
compare(Object, Object)
- Method in class ProGAL.geom3d.complex.delaunayComplex.
DelaunayComplexRotation.HeapItemComp
compareTo(BnBNode)
- Method in class ProGAL.proteins.beltaStructure.bnb.
BnBNode
cond()
- Method in class ProGAL.math.
SingularValueDecomposition
Two norm condition number
Cone
- Class in
ProGAL.geom3d.volumes
A three-dimensional cone represented by two points on its central axis.
Cone(Point, Point, double)
- Constructor for class ProGAL.geom3d.volumes.
Cone
Constants
- Class in
ProGAL.math
Constants()
- Constructor for class ProGAL.math.
Constants
Constraint
- Interface in
ProGAL.proteins.beltaStructure.bnb
contains(Object)
- Method in class ProGAL.dataStructures.
Set
contains(Point)
- Method in class ProGAL.geom2d.
Circle
contains(Circle)
- Method in class ProGAL.geom2d.
Circle
contains(Point)
- Method in class ProGAL.geom2d.
ConvexPolygon
returns true if point p is inside the convex polygon
contains(Point)
- Method in class ProGAL.geom3d.
Triangle
contains(Point)
- Method in class ProGAL.geom3d.volumes.
LSS
contains(Point)
- Method in class ProGAL.geom3d.volumes.
Sphere
Returns true if the given point is in the sphere.
contains(int)
- Method in class ProGAL.proteins.belta.
SecondaryStructure.SSSegment
containsBigPoint()
- Method in class ProGAL.geom3d.complex.
CTetrahedron
For computational convenience, the representation of a complex is based on a big tetrahedron that encloses all vertices.
containsBigPoint()
- Method in class ProGAL.geom3d.complex.
CTriangle
containsBigPoint()
- Method in class ProGAL.geomNd.complex.
Tessel
containsNone(List<Point>)
- Method in class ProGAL.geom3d.volumes.
Sphere
Returns true if none of the given points is in the sphere.
containsPoint(Point)
- Method in class ProGAL.geom3d.complex.
CEdge
containsPoint(CVertex)
- Method in class ProGAL.geom3d.complex.
CTetrahedron
containsPoint(CVertex)
- Method in class ProGAL.geom3d.complex.
CTriangle
containsPoint(Vertex)
- Method in class ProGAL.geomNd.complex.
Tessel
containsStrand(int)
- Method in class ProGAL.proteins.belta.
SheetTopology
Return true if the specified strand is in this sheet.
containsTriangle(CTriangle)
- Method in class ProGAL.geom3d.complex.
CTetrahedron
ConvexPolygon
- Class in
ProGAL.geom2d
ConvexPolygon()
- Constructor for class ProGAL.geom2d.
ConvexPolygon
ConvexPolygon(Polygon)
- Constructor for class ProGAL.geom2d.
ConvexPolygon
creates a convex hull of a simple polygon in O(n) time
ConvexPolygon(Point, Point, Point)
- Constructor for class ProGAL.geom2d.
ConvexPolygon
creates a convex polygon with given three points as corners (counterclockwise)
ConvexPolygon(PointSet, ConvexPolygon.ConvexHullAlgorithm)
- Constructor for class ProGAL.geom2d.
ConvexPolygon
creates a convex hull of a set of points Jarvis March O(hn) Grahams Scan O(nlogn)
ConvexPolygon.ConvexHullAlgorithm
- Enum in
ProGAL.geom2d
coords
- Variable in class ProGAL.proteins.
PDBFile.AtomRecord
coplanar(Point, Point, Point, Point)
- Static method in class ProGAL.geom3d.
Point
Returns true if four specified points are in the same plane
Corner
- Class in
ProGAL.geom3d.tessellation.BowyerWatson
Corner(Tet, PointWeighted)
- Constructor for class ProGAL.geom3d.tessellation.BowyerWatson.
Corner
cornerIdx(PointWeighted)
- Method in class ProGAL.geom3d.tessellation.BowyerWatson.
Tetr
Return the index of the specified corner-point and -1 if p is not a corner.
corners
- Variable in class ProGAL.geom3d.tessellation.BowyerWatson.
Tet
corners
- Variable in class ProGAL.geom3d.tessellation.BowyerWatson.
Tetr
cornerSides
- Variable in class ProGAL.geom3d.tessellation.BowyerWatson.
Tet
cornerSides[i] indicates the sign of orient(corners[i+1%4],corners[i+2%4],corners[i+3%4],corners[i]).
cornerSides
- Variable in class ProGAL.geom3d.tessellation.BowyerWatson.
Tetr
cornerSides[i] indicates the sign of orient(corners[i+1%4],corners[i+2%4],corners[i+3%4],corners[i]).
covalentBonds()
- Method in class ProGAL.proteins.structure.
AminoAcidChain
covalentBonds()
- Method in class ProGAL.proteins.structure.
Atom
create4x4ColumnMatrix(Vector, Vector, Vector, Vector)
- Static method in class ProGAL.math.
Matrix
createAndDrawDelaunay(List<Point>)
- Static method in class ProGAL.geomNd.complex.delaunayComplex.
BowyerWatson
Convenient static method for creating delaunay tessellation of a point-set and if its 2D or 3D also displaying it.
createBalancedHistogram(List<Double>, int)
- Static method in class ProGAL.statistics.
Histogram
Construct an IrregularHistogram with min-value and bin-widths such that each bin contains roughly the same number of values if the values are added.
createBoundingBox_Covariance(PointList)
- Static method in class ProGAL.geom3d.volumes.
OBB
createBoundingCylinder_CovarianceFit(PointList)
- Static method in class ProGAL.geom3d.volumes.
Cylinder
createBoundingLSS(PointList)
- Static method in class ProGAL.geom3d.volumes.
LSS
createBoundingLSS_covariance(PointList)
- Static method in class ProGAL.geom3d.volumes.
LSS
createBoundingLSS_MaxDist(LSS, LSS)
- Static method in class ProGAL.geom3d.volumes.
LSS
createBoundingRSS_covariance(PointList)
- Static method in class ProGAL.geom3d.volumes.
RSS
createBoundingRSS_covariance(RSS, RSS)
- Static method in class ProGAL.geom3d.volumes.
RSS
createBoxFromBases(Vector[], List<Point>)
- Static method in class ProGAL.geom3d.volumes.
OBB
Creates a bounding box enclosing the points in
points
using the supplied bases.
createColumnMatrix(Vector, Vector, Vector)
- Static method in class ProGAL.math.
Matrix
createControlPanel()
- Method in class ProGAL.geom3d.viewer.
Camera
createDelaunay(List<Point>)
- Static method in class ProGAL.geomNd.complex.delaunayComplex.
BowyerWatson
Convenient static method for creating delaunay tessellation of a point-set
createDiff(Vector, Vector)
- Static method in class ProGAL.geom2d.
Vector
createFromPDB(PDBFile, SheetTopology)
- Static method in class ProGAL.proteins.beltaStructure.
CanonicalSheet
createIdentityMatrix(int)
- Static method in class ProGAL.math.
Matrix
createJ2DSceneInFrame()
- Static method in class ProGAL.geom2d.viewer.
J2DScene
Create a frame containing a canvas, display it and return the J2DScene object shown in the frame.
createJ3DSceneInFrame()
- Static method in class ProGAL.geom3d.viewer.
J3DScene
Create a frame containing a canvas, display it and return the J3DScene object shown in the frame.
createMinRadCylinderFromDirection(PointList, Vector)
- Static method in class ProGAL.geom3d.volumes.
InfCylinder
Assumes dir is normalized
createRandomMatrix(int)
- Static method in class ProGAL.math.
Matrix
createRotatedVector(double)
- Method in class ProGAL.geom2d.
Vector
createRotationMatrix(double, Vector)
- Static method in class ProGAL.math.
Matrix
createRowMatrix(Vector, Vector, Vector)
- Static method in class ProGAL.math.
Matrix
createSum(Vector, Vector)
- Static method in class ProGAL.geom2d.
Vector
createTree(double)
- Method in class ProGAL.geom3d.complex.alphaComplex.
VoidTree
cross(Vector)
- Method in class ProGAL.geom3d.
Vector
Get the cross-product of this vector and v (without changing this object).
crossProduct(Vector, Vector)
- Static method in class ProGAL.geom2d.
Vector
crossThis(Vector)
- Method in class ProGAL.geom3d.
Vector
Get the cross-product of this vector and v and store the result in this vector (changes this object).
crossThis(Vector)
- Method in class ProGAL.geom3d.
Vector.ImmutableVector3d
CTetrahedron
- Class in
ProGAL.geom3d.complex
An extension of the normal Tetrahedron that is used in complexes.
CTetrahedron(CVertex, CVertex, CVertex, CVertex)
- Constructor for class ProGAL.geom3d.complex.
CTetrahedron
CTriangle
- Class in
ProGAL.geom3d.complex
CTriangle(CVertex, CVertex, CVertex, CTetrahedron, CTetrahedron)
- Constructor for class ProGAL.geom3d.complex.
CTriangle
curChainID
- Variable in class ProGAL.proteins.
PDBFile.SheetRecord
curResSeq
- Variable in class ProGAL.proteins.
PDBFile.SheetRecord
cutArealYZ()
- Method in class ProGAL.geom3d.volumes.
OBB
CVertex
- Class in
ProGAL.geom3d.complex
CVertex(Point)
- Constructor for class ProGAL.geom3d.complex.
CVertex
CVertex(Point, boolean)
- Constructor for class ProGAL.geom3d.complex.
CVertex
CVertex.DegenerateCase
- Enum in
ProGAL.geom3d.complex
Cylinder
- Class in
ProGAL.geom3d.volumes
Cylinder(Point, Point, double)
- Constructor for class ProGAL.geom3d.volumes.
Cylinder
Cylinder(LineSegment, double)
- Constructor for class ProGAL.geom3d.volumes.
Cylinder
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